Evolution of bacterial recombinase A ( recA ) in eukaryotes explained by addition of genomic data of key microbial lineages

Abstract

Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria-eukaryote) and/or secondary (eukaryote-eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium. We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

“…We also identified at least eight proteins likely involved in mitochondrial DNA recombination and/or repair, notably including an ortholog of the previously identified alphaproteobacteria-affiliated RecA proteins occurring in mitochondria of certain protists and plants (Additional file 3: Figure S1 (B)). The phylogenetic distribution and affinity of mitochondrial RecA has previously been studied by Hofstatter et al [84], who concluded that the protein has likely been secondarily lost in Discoba.…”

Too Much Eukaryote LGT

“…In secondary endosymbiosis, there exist clear and well‐known examples for such nested phylogenies that are furthermore independently corroborated by the presence of novel organelles (secondary plastids) in the recipient lineages. For example, the symbiotic origin of red secondary plastids generates trees in which plastid‐derived genes of diatoms branch nested within red algae, and the symbiotic origin of green secondary plastids generates trees in which plastid‐derived genes of chlorarachniophytes branch nested within chlorophytes . There are many such examples in the literature .…”

De novo Sequencing, Assembly, and Annotation of the Transcriptome for the Free‐Living Testate Amoeba Arcella intermedia

“…This pattern is common between Arcella and Dictyostelium, and many eukaryotic repair machineries are actually derived from archaea and are conserved between eukaryotes and prokaryotes (Hofstatter et al. ; Makarova et al. ).…”